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Davide Risso

@davi1893.bsky.social
577 followers 111 following 20 posts
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Reposted by Davide Risso
Helena Lucia Crowell @helucro.bsky.social · 17/06/2026
Little blog post, preprint included, re: spatial/image Bioc hackathon on a little Venetian island — Thank you @wkhuber.bsky.social and especially @davi1893.bsky.social (and Elena!) for organizing and securing this 🤩 location 🤩 — Let’s do it again!
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Davide Risso @davi1893.bsky.social · 06/02/2026
Registration is now open! See: csama2026.bioconductor.eu/registration...
csama2026.bioconductor.eu
CSAMA 2026 Biological Data Science
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Davide Risso @davi1893.bsky.social · 23/12/2025
We have an amazing faculty, including @wkhuber.bsky.social @csoneson.bsky.social @helucro.bsky.social @jorainer.bsky.social and more!
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Davide Risso @davi1893.bsky.social · 23/12/2025
This year's CSAMA Biological Data Science Summer School in Brixen takes place 24-29 May 2026. Topics: single-cell and spatial omics, statistics, multi-omics, ML/AI, all very hands-on using R / Bioconductor! More info: csama2026.bioconductor.eu Registration: 1 Feb 2026! @bioconductor.bsky.social
csama2026.bioconductor.eu
CSAMA 2026 Biological Data Science – CSAMA 2026 Biological Data Science
22nd Edition Bressanone-Brixen, Italy 24-29 May 2026
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Bioconductor @bioconductor.bsky.social · 18/09/2025
EuroBioC2025 is in full swing here in Barcelona! Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow! #EuroBioC2025 #Bioconductor #OpenScience #Community
EuroBioC2025 group photo on PRBB terrace with sea in background.EuroBioC2025 welcome in PRBB auditorium by host Robert Castelo, showing slides with conference sticker and sponsor logos.EuroBioC2025 hexwall banner with the hexwall creator Kevin Rue-Albrecht standing beside it.EuroBioC2025 carved wooden keyring, a gift for all participants, created by Annekathrin Nedwed.
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Bioconductor @bioconductor.bsky.social · 20/06/2025
📣 Late-breaking poster call for #EuroBioC2025 is now open! Submit by July 11 to present your work in Barcelona this September. 🔗 forms.gle/ewTGdKzB2xyE... 📅 Notifications by July 15 #Bioconductor #Bioinformatics
forms.gle
EuroBioC2025 late-breaking poster abstract submission
Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…
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Reposted by Davide Risso
Boyi Guo (郭博逸) @boyiguo.bsky.social · 06/06/2025
🤔Could quality control create more harm than good? We explore this question in the context of #SRT. SpotSweeper is developed to combat implicit selection bias. Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social 👉: bsky.app/profile/mict...
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Reposted by Davide Risso
Katie Mack @astrokatie.com · 29/05/2025
Everyone involved in trying to pass off that ChatGPT-extruded disinformation manifesto as a scientific report should be, at the very least, barred from public office for life. The MAHA report is dangerous criminal misconduct and an offence to the process of science.
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Reposted by Davide Risso
David Pfau @davidpfau.com · 28/05/2025
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
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Reposted by Davide Risso
ProPublica @propublica.org · 29/05/2025
THREAD 🧵 Internal State Department records show that months of warnings have become a reality: The Trump administration’s sudden withdrawal of foreign humanitarian aid has brought about death, violence and unrest. 1/
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Reposted by Davide Risso
Carl T. Bergstrom @carlbergstrom.com · 29/05/2025
22 years ago I pivoted from working on antibiotic resistance to pandemic viruses. Since then, I've argued that if we care about saving US lives in expectation, advance capacity for producing bird flu vaccine offers by far the greatest expected return on investment. ... We were so goddamn close.
npr.org
Trump administration cancels plans to develop a bird flu vaccine
The Department of Health and Human Services is ending a $766 million contract with the vaccine company Moderna to develop an mRNA vaccine for flu strains with pandemic potential, including bird flu.
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Reposted by Davide Risso
Paul Gardner @ppgardne.bsky.social · 29/05/2025
This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.
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Reposted by Davide Risso
Michael Baym @baym.lol · 24/05/2025
I appreciate the offers from other scientists to help Harvard (students, labs, etc) through this attack, but what would be most helpful is for you to use your position to contact your elected representatives and make it clear this fight isn't just Harvard, it will affect you, and their districts too
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Reposted by Davide Risso
Mark Robinson @markrobinsonca.bsky.social · 29/04/2025
Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"): www.biomedcentral.com/collections/...
biomedcentral.com
Call for papers - Benchmarks v2.0
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Davide Risso @davi1893.bsky.social · 07/04/2025
Fascinating talk by @andganna.bsky.social at #ds4hb A lot of food for thought on efficient data collection and fairness in AI for health!
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Reposted by Davide Risso
Tim Behrens @behrenstimb.bsky.social · 25/03/2025
Science is under threat in the US. @elife.bsky.social have commissioned a series of articles discussing the implications and what we can do. The first three articles are now live. More to follow: elifesciences.org/articles/106... elifesciences.org/articles/106... elifesciences.org/articles/106...
elifesciences.org
Science Under Threat in the United States: How scientists and institutions should respond
Individual researchers and university leaders need to make the case for science to their elected representatives and to the public at large.
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Reposted by Davide Risso
Cristian Pattaro @cpattaro.bsky.social · 28/02/2025
Would you like to spend a #postdoctoral fellowship in the beautiful Italian Alps doing great science? Apply for a MSCA Postdoctoral fellowship with us on #stats #biostats #genomics #epidemiology Many infos here 👇 🧵 #StatsSky #rstats #popgen #nephsky 1/n
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Reposted by Davide Risso
Nonia Pariente @npariente.bsky.social · 09/03/2025
📣📣Are you looking for a postdoc? 📣📣 Does a EU or Horizon Europe assoc country (eg UK, S Korea) seem like a good destination? These fellowships a great funding option for anyone in the 🌎 👀 Check them out - next call opens 8 May 🧪 👨‍🔬👩‍🔬 marie-sklodowska-curie-actions.ec.europa.eu/actions/post...
marie-sklodowska-curie-actions.ec.europa.eu
Postdoctoral Fellowships
The information provided on this page is a summary of the main rules and requirements for Postdoctoral Fellowships (PFs) and who can apply for them.
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Reposted by Davide Risso
Wolfgang Huber @wkhuber.bsky.social · 28/02/2025
Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona. This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software. eurobioc2025.bioconductor.org
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Bioconductor @bioconductor.bsky.social · 28/02/2025
🎨 Reminder that EuroBioC2025 Sticker Contest is still open! Deadline Mar 10. Don't miss out on the chance to have your design featured at the conference and win free registration ✨ Submit buff.ly/42JiCLN Abstracts are open for submission too! #EuroBioC2025 #RStats #Bioinformatics #StickerContest
buff.ly
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Itai Yanai @itaiyanai.bsky.social · 28/02/2025
"Your AI can’t see gorillas!" A few years ago we found that students are more likely to see the gorilla in their data if they are not also asked to test a specific hypothesis. In his blog Chiraag Gohel now shows that Chat-GPT can’t help you to find it either. chiraaggohel.com/posts/llms-e...
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Reposted by Davide Risso
Ilaria Prosdocimi @ilapros.bsky.social · 24/02/2025
In two weeks (10th March) John Burn-Murdoch will be holding a Conversation at the San Giobbe campus, Room 6A (2pm). Everyone is very welcome to join (and thanks @crisvarin.bsky.social for making this happen)!
A little poster promoting the event indicating its date and time (10 March, 2 pm, campus San Giobbe Venice, Room 6)
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Reposted by Davide Risso
Simon P. Couch @simonpcouch.com · 20/02/2025
New #rstats pkg gander is now on CRAN! gander is a coding assistant that knows how describe the objects in your global R environment. So, when you're working with data, LLMs will know the names, types, and distributions of data columns, resulting in much more effective completions.
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Reposted by Davide Risso
Bioconductor @bioconductor.bsky.social · 20/02/2025
📣 EuroBioC2025: Abstract Submissions Open! Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24. ➡️ Submit buff.ly/3EN9w6P #EuroBioC2025 #Bioinformatics #RStats #DataScience
buff.ly
European Bioconductor Conference 2025
EuroBioC2025 is the European edition of the Bioconductor conference that will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor…
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Davide Risso @davi1893.bsky.social · 19/02/2025
The package is general and can be used with any distribution of the exponential dispersion family, which includes the Gaussian, Poisson, negative binomial, and many others. More to come soon, including a @bioconductor.bsky.social wrapper to make it easier to work with single-cell RNA-seq data.
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Davide Risso @davi1893.bsky.social · 19/02/2025
The sgdGMF #rstats package is now officially on CRAN: cran.r-project.org/package=sgdGMF Please give it a try and let us know if you have any feedback!
cran.r-project.org
sgdGMF: Estimation of Generalized Matrix Factorization Models via Stochastic Gradient Descent
Efficient framework to estimate high-dimensional generalized matrix factorization models using penalized maximum likelihood under a dispersion exponential family specification. Either deterministic an...
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Reposted by Davide Risso
Bioconductor @bioconductor.bsky.social · 10/02/2025
🎨 EuroBioC2025 Sticker Contest! Unleash your creativity for the European Bioconductor Conference in Barcelona! The winning sticker will be featured on our website and handed out at the event. 🗓 Deadline: Mar 10, 2025 🏆 Prize: Free reg to EuroBioC2025 for winning design! Abstract call coming soon!
buff.ly
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Sen. Adam Schiff @schiff.senate.gov · 08/02/2025
Trump & Musk are making massive cuts to the National Institutes of Health. I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.
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Carl T. Bergstrom @carlbergstrom.com · 04/02/2025
Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com
thebullshitmachines.com
INTRODUCTION
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Carl T. Bergstrom @carlbergstrom.com · 08/02/2025
8. It is difficult to overstate what a catastrophe this will be for the US research and education systems, particular in biomedical fields. It is deliberate and wanton devastation entirely out of scale with any concern about DEI activities on campuses. The goal is destroy US universities.
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Reposted by Davide Risso
Carl T. Bergstrom @carlbergstrom.com · 08/02/2025
1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
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American Society for Virology @amersocvirology.bsky.social · 03/02/2025
Shoutout to all of the exceptional Black scientists who have contributed to and are currently contributing to virology research! Your work is vitally important to understanding basic virology controlling viral diseases worldwide! #BlackHistoryMonth
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Black Microbiologists Assoc (Black In Micro) @blackinmicro.bsky.social · 04/02/2025
A statement from the BMA Board Members to the BMA Community and Beyond. Additional alt text to follow due to the character limit.
The statement reads: We are disappointed in the rapid capitulation by some U.S. institutions and organizations to recent attacks on diversity, equity, inclusion, and access. At their core, these weak arguments are fueled by the familiar underlying assumption that people from Black, Indigenous, and other marginalized identities cannot be excellent and therefore have not ‘earned’ our place in public intellectual life. However, we have always been competent, hardworking, and creative people who have contributed positively to society at large, across sectors but especially in science. We reject these attempts at silencing and erasure and will continue to be a place of respite and community in these turbulent times. 

To our members, your talent, skills, and safety are important! To our friends and allies, you may be feeling like everything happening is out of your control, but we want you to know that your voice and actions can make a difference. We want to point you towards some immediate actions that you can take. These are the top 3 issues we are concerned about and what you can do about it if you mirror our concerns.

Freezing of federal funding and cutting grant programs for scientific research that have any connotation of being “DEI.”
The potential confirmation of RFK Jr., a vocal anti-vaccination proponent, as the head of HHS.
The American Society for Microbiology (ASM) removed their ABRCMS and IDEAAS webpages in addition to some scientist spotlights and written articles highlighting the current and historic contributions of microbiologists who are a part of marginalized communities including LGBTQIA+, Women, Indigenous and Black, as well as others page that could be considered “‘DEI”. Many have now been reinstated with changes to language (i.e. removing terms like “equity” and “marginalized”), and the statements released by ASM did not acknowledge the harm that they have caused to their members and showed no remorse for their actions.
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Davide Risso @davi1893.bsky.social · 03/02/2025
Registrations are now open! Follow the link at csama2025.bioconductor.eu/registration...
csama2025.bioconductor.eu
CSAMA 2025 Biological Data Science
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Reposted by Davide Risso
Dr Emma Hodcroft @firefoxx66.bsky.social · 01/02/2025
It's all gone. They've taken down all the CDC datasets from data.cdc.gov Data that's critical for public health & research. Data paid for by citizens. That the government now censors. "Do not fear those who tell the truth. Fear those who try to hide it. They are willing to sacrifice other things."
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Davide Risso @davi1893.bsky.social · 27/01/2025
This is a great chance to learn from long-term Bioconductor developers (including three founding members!). Registration opens on February 1st. All the info here: csama2025.bioconductor.eu
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Davide Risso @davi1893.bsky.social · 27/01/2025
Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!
CSAMA 2025 flyer
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Davide Risso @davi1893.bsky.social · 23/01/2025
I fail to see how this is unusual, it's a standard model. As for reliability and stability, I believe that we make a good case for them in the paper for our model. I have my own thoughts on ZI models but I'll save them for another time as here we do not model ZI.
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Davide Risso @davi1893.bsky.social · 22/01/2025
Of course it could be useful in other applications (e.g., DE) to have genewise dispersions and it's something that we could add in a future version of the package.
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Davide Risso @davi1893.bsky.social · 22/01/2025
Right. We currently have a global dispersion parameter. In our comparisons, this is enough to correctly estimate the latent factors (see also www.nature.com/articles/s41...).
nature.com
A general and flexible method for signal extraction from single-cell RNA-seq data - Nature Communications
Single-cell RNA sequencing (scRNA-seq) data provides information on transcriptomic heterogeneity within cell populations. Here, Risso et al develop ZINB-WaVE for low-dimensional representations of scR...
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Davide Risso @davi1893.bsky.social · 22/01/2025
Sure. If I understand your question, w_{ij} in eq.2 are optional known weights (as in weighted regression) that can be used if appropriate in the application or can be safely ignored (that's what we do in our single-cell examples in the paper). This isn't different from the basic lm() function.
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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024
🧬 🖥️ Need help for investigating tissue complexity from #spatial #transcriptomics data? Try out our #spacedeconv R package! 💻 Code: github.com/omnideconv/s... 📝 Preprint: www.researchsquare.com/article/rs-5...
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Davide Risso @davi1893.bsky.social · 21/01/2025
This work was driven by Cristian Castiglione and was a great collaboration with Lieven Clement and Alex Segers
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Davide Risso @davi1893.bsky.social · 21/01/2025
This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper: arxiv.org/abs/2412.20509 We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data
arxiv.org
Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data
Single-cell RNA sequencing allows the quantitation of gene expression at the individual cell level, enabling the study of cellular heterogeneity and gene expression dynamics. Dimensionality reduction ...
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Davide Risso @davi1893.bsky.social · 21/01/2025
This is insane, and honestly quite worrying... even (or especially?) when looking at it from this side of the ocean.
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Cristian Pattaro @cpattaro.bsky.social · 06/12/2024
❗Still one week to apply for our postdoc position in bionformatics & biostatistics @ Eurac Biomedicine in the beautiful Dolomites - hurry up! #stats 👇
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Helena Lucia Crowell @helucro.bsky.social · 04/12/2024
A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...
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Michael Hoffman @michaelhoffman.bsky.social · 28/11/2024
The UX of LEGO Interface Panels interactionmagic.com/UX-LEGO-Inte...
interactionmagic.com
The UX of LEGO Interface Panels
LEGO interface panels are beautiful, iconic, and great for learning interface design basics. I bought 52 of them from BrickLink to explore the design, layout and organisation of complex interfaces.
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Wolfgang Huber @wkhuber.bsky.social · 25/11/2024
Maintain a public archive of your old tweets that's independent of X, as a self-hosted static webpage. An R/Quarto script that reads your tweet archive (downloaded from X) & creates an HTML page. Example (w/ my own tweets 2015-24): wolfganghuber.github.io/tweets/index... github.com/wolfganghube...
Screen shot of Wolfgang Huber's tweet archive
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